In production of rod shaped elements of tobacco industry there is a necessity of transporting the elements from making machines to machines effecting further operations on them. The more diversified is the assortment of products manufactured, which causes the number of making and processing machines to be increased, the more complicated is the system of production arrangement, for various types of manufactured elements must be delivered at a certain moment to respective processing machines. Said elements, after manufacturing, are loaded into one chamber trays and then are brought into an intermediate store, from where they are transferred for further processing. From British patent description No. GB 1 234 776 it is known a system of devices, applied in factories, for transporting cigarettes loaded in one chamber trays from making machines to an intermediate store, whereas the trays are transported in baskets and before bringing the trays into the store, the trays are unloaded from the baskets. The intermediate store is provided with several independent tray unloaders, which unload assortment defined trays and cigarettes are transferred in form of mass flow to a respective groups of packing machines. Another arrangement for making and packing cigarettes has been presented in U.S. Pat. No. 5,628,162. According to the invention, a group of cigarette making machines is connected to a group of packing machines by way of traction with use of a transporter transferring trolleys with containers in which there are stacked one chamber trays, whereas cigarettes are loaded into trays on making machines, next trays are grouped in containers in a special handling device and then the containers are transferred to the trolleys. The loaded trolleys may be kept in a specified store, from where they are collected at a certain moment to a transporter which transfers them to a respective packing machine, which is also provided with a special handling device for unloading containers and transferring full trays to a packing machine, and, after emptying them, for grouping empty trays in containers and placing containers on a trolley, which is taken back to the traction transporter. From another U.S. Pat. No. 6,158,194 it is known a system for transporting rod shaped elements collected in one chamber trays in tobacco industry, especially filters, where the production line consists of a group of making machines and a group of machines for further processing the elements. The produced rod shaped elements are charged into one chamber trays in form of a cubicoid devoid of the top and one side wall, in a tray filler associated with a making machine, and then trays of one assortment of product are transferred to a special device for handling containers, where they are stacked in containers. Next the closed containers are displaced to an intermediate store comprising a significant number of stationary shelving, on which containers with full trays are positioned with use of a stacking machine which moves along the shelving. After receiving a signal the stacking machine removes a respective container off the shelving and passes it to a special handling device disposed in the zone of a production line comprising machines for processing elements, where trays are removed from a container and transferred to an unloader to empty rod shaped elements, which are then used in a processing machine. In a system according to the invention it has been ensured to facilitate direct transferring containers between handling devices located in the zone of making machines and in the zone of processing machines. Empty trays are stacked back into the container in a special handling device of the zone of processing machines, and then the container is collected by the stacking machine and located on the shelving in the zone for empty trays. After receiving a signal the stacking machine delivers a container with empty trays to a specified handling device of the zone of making machines.